#!/usr/bin/perl 
use warnings;
use strict;
use Bio::SearchIO;
use Bio::AlignIO;

my $out = ">C:/Documents and Settings/mgavi.brathwaite/Desktop/current
+/bl2seq/13117_aln1.out";
my $dir = 'C:/Documents and Settings/mgavi.brathwaite/Desktop/current/
+bl2seq/';
my $in = new Bio::SearchIO(-format => 'blast',
                           -file   => $dir.'13117_2.out',
                           -report_type => 'bl2seq');
while( my $result = $in->next_result ) {
  while( my $hit = $result->next_hit ) {
   while( my $hsp = $hit->next_hsp ) { 
     if( $hsp->length('total') > 1000 ) {
      if ( $hsp->percent_identity >= 90 ) {
       if(    $hsp->score ){
        if(     $hsp->gaps ){
         if(  $hsp->expect ){
            print  "Hit= ",    $hit->name, 
                    " Length=",     $hsp->length('total'), 
                    " Score=",        $hsp->score,"\n";
            print " Gaps=",    $hsp->gaps,
                    " Expect=",        $hsp->expect,
                    " Percent_id=", $hsp->percent_identity, "\n";
=cut
                    # $hit->name, $hit->hsps,
                                $hit->name, 
                                $hsp->length('total'), 
                                $hsp->score,
                                $hsp->gaps,
                                $hsp->expect,
                                $hsp->percent_identity;    
=cut                                
                    my $aln = $hsp->get_aln;    
                    my $alnIO = Bio::AlignIO->new(-format =>"clustalw"
+, -file => $out);
                    $alnIO->write_aln($aln);
          }
         }
        }
      }
    }
   }  
  }
}

[download]
I can get the alignment, but I also need the print data
to be prepended at the top of the $out file.

In reply to Re^2: parsing blast output by lomSpace
in thread parsing blast output by lomSpace

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